How to align a single bone between two animated empties
Aligned Bone -
This is similar to the 'Rubbery lines' project in that a curve-path with just 2 control-points (one at each end) is strung between 2 moving empties.  The northern empty is a hook which stretches the path between them.   (Blend file below)

To set it up -
Place the empties and animate them around scene as desired.  (call them  H nth  &amp;  H sth?)
Add a Nurbs path, goto Edit mode and delete it's 3 intermediate control points so there are just 2 remaining.  One at each end.
Set the path's Origin Point to the starting end. (see it's arrows in Edit mode)
Move the path so it's reasonably aligned between the two empties and that it's starting end &amp; OP are near the southern empty.
Select this empty and with SH-S, set the 3D cursor &quot;to selected&quot;.
Select the Path and use SH-S again --&gt; &quot;Selected to 3D cursor&quot;
The path's starting end should then be sitting exactly at the southern empty.
Make the empty a parent for the path.  (CTL-P)
Give the path a 'Track-to' constraint and have it 'looking at' the Northern Empty.
When played, the path should be attached to the southern empty and always looking at the northern one.
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To keep the path stretched between them -
Goto frame 1 and Select the path.  Go into Edit mode and drag the end CP up so it reaches the northern empty.
Check from the top &amp; side views (in ortho view) to see it's aligned properly.
Hook the northern empty to the path's northern CP. (CTL-H)
Play the animation again and the path should now reach both empties at all times.
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The  Bone -
At frame 1 place the bone at the path's center or wherever it's required.  Align it to the path reasonably well.
Parent the bone to the path. (child = bone)
In this example the bone was simply keyframed to keep it reasonably at the center of the path but a driver or short script may well do this automatically.